Organism : Methanococcus maripaludis S2 | Module List :
MMP0086 tfx

putative transcriptional regulator

CircVis
Functional Annotations (9)
Function System
Uncharacterized protein conserved in archaea cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
tfx tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0086
(Mouseover regulator name to see its description)

MMP0086 is regulated by 9 influences and regulates 12 modules.
Regulators for MMP0086 tfx (9)
Regulator Module Operator
MMP0527
MMP1100
150 combiner
MMP1376 150 tf
MMP0018
MMP0480
160 combiner
MMP0097
Formate
160 combiner
MMP0097
MMP1015
160 combiner
MMP0097
MMP1376
160 combiner
MMP0257
MMP1712
160 combiner
MMP0480 160 tf
MMP0480
MMP0719
160 combiner

Warning: MMP0086 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
949 5.10e+02 TacgGggtGtT
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950 2.10e+03 cttCatatt.cA.AatccccTTc
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967 8.70e-01 ATgTcgGGtaT
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968 3.20e+02 cAgGgag.aGG
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for MMP0086

MMP0086 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Uncharacterized protein conserved in archaea cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
tfx tigr/ tigrfam
Module neighborhood information for MMP0086

MMP0086 has total of 37 gene neighbors in modules 150, 160
Gene neighbors (37)
Gene Common Name Description Module membership
Antisense_10 None 2, 43, 150
MMP0038 type II secretion system protein 115, 160
MMP0039 hypothetical protein MMP0039 115, 160
MMP0040 type II secretion system protein E 115, 160
MMP0041 tfb transcription initiation factor IIB 19, 160
MMP0069 methylated-DNA--protein-cysteine methyltransferase 23, 150
MMP0086 tfx putative transcriptional regulator 150, 160
MMP0102 pcm protein-L-isoaspartate O-methyltransferase 2, 43, 150
MMP0190 hypothetical protein MMP0190 150, 159
MMP0234 hypothetical protein MMP0234 46, 160
MMP0235 hypothetical protein MMP0235 75, 160
MMP0237 hypothetical protein MMP0237 75, 160
MMP0238 hypothetical protein MMP0238 160, 166
MMP0240 hypothetical protein MMP0240 75, 160
MMP0299 hypothetical protein MMP0299 154, 160
MMP0452 hypothetical protein MMP0452 75, 160
MMP0458 hypothetical protein MMP0458 75, 160
MMP0528 hypothetical protein MMP0528 23, 150
MMP0595 hypothetical protein MMP0595 75, 160
MMP0636 hypothetical protein MMP0636 75, 160
MMP0656 hypothetical protein MMP0656 46, 160
MMP0721 ferredoxin 125, 160
MMP0722 hypothetical protein MMP0722 58, 160
MMP0723 hypothetical protein MMP0723 75, 160
MMP0783 hypothetical protein MMP0783 43, 160
MMP1019 PEGA domain-containing protein 23, 150
MMP1235 moaE molybdopterin biosynthesis MoaE 49, 55, 106, 117, 150
MMP1237 hypothetical protein MMP1237 50, 150
MMP1256 hypothetical protein MMP1256 150, 159
MMP1279 camphor resistance protein CrcB 115, 160
MMP1282 hypothetical protein MMP1282 49, 102, 106, 150
MMP1283 hypothetical protein MMP1283 49, 102, 150
MMP1294 glgA starch synthase 43, 150, 166
MMP1387 hypothetical protein MMP1387 33, 73, 150
MMP1552 3-octaprenyl-4-hydroxybenzoate carboxy-lyase 54, 150
MMP1608 hypothetical protein MMP1608 150, 160
MMP1653 hypothetical protein MMP1653 150, 166
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for MMP0086
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend